Genomic signatures of strawberry domestication and breeding

Cultivated strawberry (Fragaria x ananassa) has a brief history of less than 300 years, beginning with the hybridization of octoploids F. chiloensis and F. virginiana. Here we explored the genomic signatures of this history using whole-genome sequences of 289 wild, heirloom and modern varieties. Four non-admixed wild octoploid populations were identified, with recurrent introgression among the sympatric populations. The proportion of F. virginiana ancestry increased by 20% in modern varieties over initial hybrids, and the proportion of F. chiloensis subsp. pacifica rose from 0 to 3.4%. Effective population size rapidly declined during early breeding. Meanwhile, divergent selection for distinct environments reshaped wild allelic origins in 21 out 28 chromosomes. Despite 20 breeding cycles since the initial hybridization, more than half of loci underlying yield and fruit size are still not under selection. These insights add clarity to the domestication and breeding history of what is now the most widely cultivated fruit in the world.